your call is expected to be arrayQualityMetrics(expressionset = ntest, outdir = "Report_ntest", force = TRUE) note: no quotes around ntest. b On 8 March 2012 12:12, henlen [guest] <guest at="" bioconductor.org=""> wrote: > > when i running arrayQualityMetrics, i met a broblem like this, > Error in function (classes, fdef, mtable): > unable to find an inherited method for function "platformspecific", for signature "character". > I want to use arrayQualityMetrics to analyse Affymetrix data- after preprocessing. > > Before using > arrayQualityMetrics, i used ReadAffy on my CEL file to get an ?AffyBatch abject, > then used RMA algorithm on the object to obtain a preprocessed dataset, > finally called arrayQualityMetrics to analyse the preprocessed, then the error appeared. > > when called ReadAffy and rma, no erros found, > and i can call the arrayQualityMetrics on the MLL.A subject provided in the data package ALLMLL without any error. > > Following is the commonds i used and the results, > GSM162264.CEL is the CEL file got from GEO. > >>test <- ReadAffy("GSM162264.CEL", > ? ? ? ? ? ? ? ? ?widget=getOption("BioC")$affy$use.widgets, > ? ? ? ? ? ? ? ? ?celfile.path=NULL, > ? ? ? ? ? ? ? ? ?sampleNames=NULL, > ? ? ? ? ? ? ? ? ?phenoData=NULL, > ? ? ? ? ? ? ? ? ?description=NULL, > ? ? ? ? ? ? ? ? ?notes="", > ? ? ? ? ? ? ? ? ?rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, > ? ? ? ? ? ? ? ? ?verbose=FALSE,sd=FALSE, cdfname = NULL) > >>ntest = rma(test) > >>arrayQualityMetrics(expressionset = "ntest", > ? ? ? ? ? ? ? ? ? ? outdir = "Report_ntest", > ? ? ? ? ? ? ? ? ? ? force = TRUE) > The report will be written into directory 'Report_ntest'. > Error in function (classes, fdef, mtable) ?: > ?unable to find an inherited method for function "platformspecific", for signature "character" > > >>test > AffyBatch object > size of arrays=732x732 features (17 kb) > cdf=Maize (17734 affyids) > number of samples=1 > number of genes=17734 > annotation=maize > notes= > >>ntest > ExpressionSet (storageMode: lockedEnvironment) > assayData: 17734 features, 1 samples > ?element names: exprs > protocolData > ?sampleNames: GSM162264.CEL > ?varLabels: ScanDate > ?varMetadata: labelDescription > phenoData > ?sampleNames: GSM162264.CEL > ?varLabels: sample > ?varMetadata: labelDescription > featureData: none > experimentData: use 'experimentData(object)' > Annotation: maize > > so, how should i fix the problem, expecting for your help, appreciate very much. > > ?-- output of sessionInfo(): > > R version 2.14.2 (2012-02-29) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United States.1252 ? ?LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_United States.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > ?[1] vsn_3.22.0 ? ? ? ? ? ? ? ? limma_3.10.3 ? ? ? ? ? ? ? hgu133acdf_2.9.1 ? ? ? ? ? ALLMLL_1.2.11 > ?[5] annotate_1.32.1 ? ? ? ? ? ?affyPLM_1.30.0 ? ? ? ? ? ? preprocessCore_1.16.0 ? ? ?gcrma_2.26.0 > ?[9] affyio_1.22.0 ? ? ? ? ? ? ?maizecdf_2.9.1 ? ? ? ? ? ? AnnotationDbi_1.16.18 ? ? ?affy_1.32.1 > [13] arrayQualityMetrics_3.10.0 Biobase_2.14.0 ? ? ? ? ? ? BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > ?[1] beadarray_2.4.1 ? ? Biostrings_2.22.0 ? Cairo_1.5-1 ? ? ? ? cluster_1.14.2 ? ? ?DBI_0.2-5 > ?[6] genefilter_1.36.0 ? grid_2.14.2 ? ? ? ? Hmisc_3.9-2 ? ? ? ? hwriter_1.3 ? ? ? ? IRanges_1.12.6 > [11] KernSmooth_2.23-7 ? lattice_0.20-0 ? ? ?latticeExtra_0.6-19 RColorBrewer_1.0-5 ?RSQLite_0.11.1 > [16] setRNG_2009.11-1 ? ?splines_2.14.2 ? ? ?survival_2.36-12 ? ?SVGAnnotation_0.9-0 tools_2.14.2 > [21] XML_3.9-4.1 ? ? ? ? xtable_1.7-0 ? ? ? ?zlibbioc_1.0.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor